The shots of the public execution are due to be shown on Panorama on 1 April.
The documentary was triggered by controversy over the Saudi dissident Mohammed al-Masari, 49, whose deportation from London was ordered after he allegedly attempted to undermine the Saudi government.
Mr Masari was tortured for six months and lost his job as a professor of physics after he established the Committee for the Defence of Legitimate Rights, a human rights group, in Saudi Arabia in 1993.
The Home Office is now reconsidering its decision to deport the Islamic activist, who has also embarrassed the British government by repeatedly denouncing the "corruption" of the Saudi royal family.
The documentary is likely to further sour relations between Britain and Saudi Arabia. In its listing, the BBC describes the country as "what many consider to be the world's most brutal and despotic regime".
It continues: "Last year nearly 200 people were publicly beheaded in Saudi, many for offences involving trafficking, alcohol and adultery, yet the British government does not dare to criticise its close Middle East ally for fear of losing lucrative arms contracts."
UK exports to Saudi Arabia totalled pounds 1.5bn in 1994, but Saudi Arabia has indicated that if the Home Office refuses to deport Mr Masari it could withdraw business contracts with Britain.
Roger Gale, chairman of the influential Tory backbench media committee, said yesterday: "If they are going to show decapitation I would regard this as wholly gratuitous unpleasantness.
A BBC spokeswoman said: "It is not sensational. You do not actually see heads rolling on pavements."Reuse content